Compromised
by Eleonore Magilinon
Summary: The story follows the end of "Prisoner's Dilemma" and tells how the matter of John being kidnapped by his former partner grows into the situation where the safety of the Machine itself becomes compromised. How will it turn out with a certain federal agent still in the picture? Allies and enemies old&new all play their roles... And don't forget - you're being watched. Different POVs


**A/N**: _This story starts right after the end of "Prisoner's Dilemma" and will most certainly become an AU after the next episode, although right now this turn of events is possible, though unlikely. It should be noticed that while it looks like agent Donnelly was shot in the head, there are two arguments proving that wrong – there was no sign of a bullet hole in his head when he is shown after the shots, and we hear him moaning after both shots – from the hit to the head you die instantly._

_I will be using all clues and pieces of evidence on the matter of the government officials knowing about the Machine, and also CIA and the private intelligence network Donnelly was investigating, together with my own interpretation of the hints given to us in both seasons to explain how the matter of John being kidnapped by his former partner turned into the situation where the safety of the Machine itself became compromised._

_Another thing - you shouldn't pay too much attention to the main character tags, since there will be five main characters and way more than five different POVs as others tag along with their respective roles - both allies and enemies._

_Enjoy the story!  
P.S. Reviews are highly welcomed._

* * *

**Chapter 1: Questions.**

* * *

When Joss regained her consciousness, her whole body was aching. It was dark, she was at the backseat of a broken car turned upside down, and her left hand was still tied to that car by a pair of handcuffs.

She remembered how Donnelly got a phone call just before the trunk smashed into them, how the car was turning, making three full circles before crashing down on the ground. How after that a woman with a gun appeared and shot Donnelly twice, then came to John, addressing him playfully – and injected something into his neck.

It was after that she lost consciousness because of the wounds.

John.

John was not lying next to her, as he was after the crash, he was nowhere to be found when she looked outside, and the handcuff that used to tie her hand to John's was swinging freely over her right hand. She barely could move but she had to get out of the car. It was clear that if that woman, whoever she was, did not kill John on the spot, she took him with her – and the way she chose to do that spoke for itself. Even a glimpse Joss took at her movements, the way she handled her weapon – that person was a trained professional, and it was nasty whichever side she was working for. If she was CIA... Joss knew what would happen next, firsthand knowledge she would like to forget, and yet the guilt for getting John into that situation was always there with her. And even if she wasn't... Damn, if it were to be like that, John was safer at Rikers. There they at least knew where he was and who they were dealing with. Oh, God...

She had to get out and contact Finch. He should be able to do something, at least he should be able to find out who that woman was and where to begin looking for John.

Searching the dead man's pockets wasn't something she would have liked doing, but she slipped her free hand to the front seat where Donnelly was lying, and got the key. Then she crawled out of the car.

The area where they were ambushed was chosen strategically well. Just under the bridge, no apartment buildings nearby. Only abandoned houses with boarded up windows and a construction site, obviously empty at that time of night – that meant no witnesses. And – she was guessing – no cameras as well. Just a block from here the nightlife of the never-sleeping city was blossoming with thousands of voices, car engine's sounds, traffic lights and glittering flash-boards, and in here there were just pale light of the street lamps – and nothing more. Dead, uneasy silence.

Her own phone was taken away by Donnelly, along with John's, when he arrested them, and she saw him placing both of them into the glove compartment of the car.

And it was when she bended over Donnelly's body to get the phone out that she heard it – a slight moan escaping the man's lips. She hurried to check his pulse, and, to her surprise, there it was – a definite pulsation running under her fingers placed on his neck. She slipped her hand under his suit and spotted a protective vest covering the spot on the higher chest where he was shot – no doubt, he decided to take precaution coming after the dangerous "man in a suit".

She dragged him out and rested him against the car next to the crashed one. He was still unconscious.

When she took the phone out there were a dozen notifications of missed calls from unidentified number on the screen – without a doubt, all coming from Finch. She dialed him.

"Yes, detective?" the answer came before the first beep. A lot of strain could be heard the voice, as well as eagerness to get information. "What happened? Are you and John safe?"

"Donnelly found us out after all. He arrested us both, and he was transporting us to a safe-house..."

"I know that, detective. I was trying to warn agent Donnelly, but I was too late..."

"It was you who called him right before?.. Well, the next moment a trunk run into the car, and when we landed on the ground after taking a few turns, a woman came. She was a highly trained professional, special forces or worse. She took John, Finch! She shot Donnelly and then she injected something into John's neck. I don't know what happened afterwards, I lost consciousness, but when I woke up, she and John'd dissapeared."

"What can you tell about the woman, detective?"

'Tall, about 70 inches minus high-heels, slim, red haired – and she knew John. I mean she knew him personally, she has addressed him like someone she's been close to." _Hey lover, miss me?_ – yes, that called for a very close acquaintance. And it was pointing at the most likely choice of her employers. But there still should be a chance, a way...

"I will start searching for someone matching that description as soon as I can." The voice on the other end of the phone was impassive, the same way she had already gotten used to hearing, but it did not deceive her – that strange guy with a limp and a stone cold brilliance when it came to computers and resources was as worried for his partner as she was.

"How long was I out?" she asked him, trying to calculate the damage done by the time already lost.

"Not long, detective. Approximately ten minutes. I am now returning to start searching for the woman in question, but detective Fusco is about to come to your location and take you with him." Carter did not even ask how he was aware of their location, somehow he always knew. But something ticked off in that last sentence.

"About that" Joss realized she did not tell it before, and Finch probably assumed the same thing she did, "there's another matter – agent Donnelly is alive. He was wearing a vest" she explained. "Right now he is unconscious, but he needs medical help, we can't leave him here." And there was also a matter of agent Donnelly knowing about John – and about her. She was ready to take the responsibility for her actions, if needed – though she still did not think she had done something wrong – but even if it had to be done, she was willing to add some more charges to the list just to gain some time to help rescue John.

"You are right, detective, we can't. Then you will take him to one of the safe-houses, I will tell coordinates to detective Fusco, and I will organize proper medical help ready at the place. I will contact you when you get there, your help will most certainly be needed with the identification of the woman who took John. Also, I expect you to take care of the car."

Right. Blood all over the cabin, solid evidence of three people being inside at the time of the crash – and a way of identifying them. Truth will get out eventually, but they could not afford it getting out tpoo soon.

"We will." She signed to herself. Even after all the experience she had gotten while working with those two, she still disliked doing things that she herself would label as criminal activity only a year ago. She liked serving the law, not breaking it.

And then she knew she did not regret what she was doing – because the reason was definitely worth it. Helping a good man always was. Wherever he was right now...

The sound of car engines broke the silence of the night, and while Carter reached for Donnelly's gun just in case, the next moment she could recognize in the transparent white of approaching car's front lights a police patrol vehicle. She knew its number.

"Fusco's here" she told Finch.

"Then I will contact you later, detective" came the answer.

"And we _will_ most definitely find John" he added.

She did not expect for him to say that, he was not the likely person to give words of comfort or empty assurances – and she knew how the situation was looking. But she was grateful for those words. She needed to hear them.

"Oh yes, we will." She said before ending the call. And she believed those words.

* * *

When he returned to his senses, the first thing Nicolas Donnelly heard was an unfamiliar voice coming from ahead while the whole place was moving forward at a steady pace – that identified the location as the backseat of a moving car.

"So that woman run into you with the trunk, and then took the wonder boy? And you say she knew him?"

The tone of that voice was not the concentrated, business-like one the detectives and agents used while getting the details of the case, it sounded more like someone discussing a rumor with a friend over a beer, and that was decidedly not what he would have expected. He would have expected voices of FBI investigators, he would have expected voices of the medical officers or, in worst case scenario, "specialists" assigned to get information out of him. And that voice meant that something out of the expected was happening – thus he should try to understand the situation so he can figure the best way to act in it. With that he tried not to make any movements that would reveal he had regained consciousness, and listened.

"Yes, that was how it was. And she was also a trained professional, most probably special forces or something of the sort." That was Carter's voice, coming from the left. She was sitting next to him.

What were they talking about? Wasn't all the trunk business simply a way to rescue the man in a suit when he arrested him? He had to admit that though he understood that arresting that man would not be easy, he did not expect for his accomplices to act so boldly.

"Something of the sort? You mean, she's his buddy from CIA?" came that nonchalant voice again.

"She might be." He could discern an anxiety in her answer, though she tried to hide it. She was genuinely worried. And that meant she did not expect the whole thing. That proved it – she was tricked by the man in a suit after all. And he had told her so!

"Well, that doesn't look good" the voice commented, also sounding concerned.

"Anyway, Finch is searching for possible candidates right now" Carter hurried to add, "when we find that person, we will find out who she is working for."

"And the guy over there?" They were talking about him now. "He is the federal agent who caught John, isn't he? And he knows about him now, and about you too. So why are we taking him, again?"

Good question. From their point of view when they had found he was still alive, they should have finished the job.

"Because he needs medical help, Fusco. I don't know if you ever got into a car crash and got shot twice, but I should tell you that getting shot even with a vest on at close range is no laugh."

"I was shot four times at close range, just so you know." Fusco, Fusco... The name of Carter's partner in NYPD. He should have guessed. Although that guy did not give an impression of anything close to professional, the type that gets by more or less, not the one to put any extra effort in his job. Another proof that looks can be deceiving. "I got the point. And next thing, you gonna tell me we are dropping him at the hospital? So that the next day he can come and arrest you?"

"That is why we're not taking him to the hospital, at least not for now. But he is getting medical care, Finch said he will take care of that."

That classified as a kidnapping of a federal agent. And yet – the way Carter was set to help him... That most probably was her own decision, he was sure people who hired the man in a suit would not support the idea. He was not wrong in evaluating Joss Carter, she _was_ a very talented and honest police detective, vigilant in pursuing criminals and helping people, someone who valued human lives. She just allowed herself to be deceived. Nor she nor her partner realized that the ones who would be waiting for them at their destination would not be medical stuff but trained assassins ordered to dispose of him – and them, if they would try to intervene or back out, seeing those men for who they were.

"The glasses guy said so? Then he will, no joke."

Glasses guy named Finch, already mentioned twice in the conversation. Yet another person from that private intelligence organization, he should remember that, in case he would have a chance to use that information later.

Also, there was a matter of the person who called him on his cell just before the crash. He called himself a partner of a man in a suit, and he said to him stop his car, saying that "he had a source which told him he was in grave danger"... Unless it was a way to distract him – but that was not needed, when a trunk was set to hit the car in mere seconds – it just did not end up, no matter how one looked at those words.

Why would somebody try to warn him? And how would that person obtain the information about him being targeted? Another person being tricked by them who realized the truth quicker than detective Carter? That was too much of a coincidence, plus in that case he would not call himself a partner of the man in the suit. It was not a good credit to gain his trust, and there was no reason for that person to sabotage his partner's escape plan.

And how did he even get his number? FBI agent's phone number is no public information.

His head started to ache. He was barely conscious, and with all the questions piling up and pieces refusing to come together the situation just felt surreal.

"So, what's next?" he tried to concentrate on the voice of Carter's partner to clear his head and ease the pain.

"We don't know yet. It depends on who that woman who kidnapped John is and what she and the ones she works for want from him."

There was a pause.

"He'll come through, Carter" her partner added finally. "You know him – he always does. He'll manage to get away somehow. And if not – we gonna help him."

"Yeah, I know" she answered. After that the silence fell.

The silence that helped Donnelly gather his thoughts.

Let's see. Excluding the strange phone call, everything else pointed to Carter and her partner being used by the private intelligence organization he was investigating, and right now they were heading to a location where people from that organization were waiting for them. So his only chance to survive was to escape before they reach their destination.

He took notice of the sounds that could be heard outside, quite a lot of them, which called for a crowded place, and no sound of passing cars, which suggested one way street – best option for him.

He had an element of surprise on his side, Carter would hesitate to shoot him, afraid that she would kill him. He just needed to choose the right time to act...

At that moment the car jolted heavily, and he lost consciousness once again.


End file.
